Hello,
I am having an issue with getting the FastQC tool to work with Galaxy on
our server. I downloaded the FastQC files (version 0.8.0) and changed the
directory that the wrapper script looks for the 'fastqc' executable in, but
when we run a job with it we have been getting the following output:
"Started analysis of Clip
Approx 5% complete for Clip
Approx 10% complete for Clip
...
...
Approx 95% complete for Clip
Approx 100% complete for Clip
Analysis complete for Clip
(.:9754): Gtk-WARNING **: cannot open display: "
And then the job shows as failed in Galaxy. The output .dat file just has
that same output/error message in it (though it seems to indicate it got to
100%). Also when I try to execute the fastqc file directly (albeit with no
arguments) I get this:
"Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation
which requires it.
at
java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173)
at java.awt.Window.<init>(Window.java:437)
at java.awt.Frame.<init>(Frame.java:419)
at java.awt.Frame.<init>(Frame.java:384)
at javax.swing.JFrame.<init>(JFrame.java:174)
at
uk.ac.bbsrc.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:271)
at
uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102)"
Both errors seem to have something to do with the graphical GUI component
of FastQC (which I have seen some screenshots for on the FastQC webpage).
If this application is GUI-driven how did the online PSU Galaxy get it to
work with their wrapper script when the tools are run in a command-line
environment with no X11 or Gtk? Essentially I'm just wondering what steps
I'm missing here to getting this to work with our Galaxy mirror, other than
just dropping the executable in place? Any suggestions?
Thanks,
Josh
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